fitDO {metagenomeSeq} | R Documentation |
This function returns a data frame of p-values, odds ratios, lower and upper confidence limits for every row of a matrix. The discovery odds ratio is calculated as using Fisher's exact test on actual counts. The test's hypothesis is whether or not the discovery of counts for a feature (of all counts) is found in greater proportion in a particular group.
fitDO(obj, cl, norm = TRUE, log = TRUE, adjust.method = "fdr", cores = 1, ...)
obj |
A MRexperiment object with a count matrix, or a simple count matrix. |
cl |
Group comparison |
norm |
Whether or not to normalize the counts - if MRexperiment object. |
log |
Whether or not to log2 transform the counts - if MRexperiment object. |
adjust.method |
Method to adjust p-values by. Default is "FDR". Options
include "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr",
"none". See |
cores |
Number of cores to use. |
... |
Extra options for makeCluster |
Matrix of odds ratios, p-values, lower and upper confidence intervals
data(lungData) k = grep("Extraction.Control",pData(lungData)$SampleType) lungTrim = lungData[,-k] lungTrim = lungTrim[-which(rowSums(MRcounts(lungTrim)>0)<20),] res = fitDO(lungTrim,pData(lungTrim)$SmokingStatus); head(res)